Author: bugman
Date: Tue Mar 10 10:15:35 2015
New Revision: 27802
URL: http://svn.gna.org/viewcvs/relax?rev=27802&view=rev
Log:
Modified the spectrum.read_intensities user function backend to be more robust.
This affects the generic formatted peak lists, via the
lib.spectrum.peak_list.intensity_generic()
function. The peak list reading will now continue reading the file after
corrupted lines have been
encountered.
Modified:
trunk/lib/spectrum/peak_list.py
Modified: trunk/lib/spectrum/peak_list.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/spectrum/peak_list.py?rev=27802&r1=27801&r2=27802&view=diff
==============================================================================
--- trunk/lib/spectrum/peak_list.py (original)
+++ trunk/lib/spectrum/peak_list.py Tue Mar 10 10:15:35 2015
@@ -1,6 +1,6 @@
###############################################################################
# #
-# Copyright (C) 2004-2014 Edward d'Auvergne #
+# Copyright (C) 2004-2015 Edward d'Auvergne #
# Copyright (C) 2008 Sebastien Morin #
# Copyright (C) 2013 Troels E. Linnet #
# #
@@ -112,9 +112,13 @@
for line in file_data:
# Loop over the intensity columns, storing the data.
intensity = []
+ data_flag = False
for i in range(len(data_col)):
# Extract the data for the single line (loop of a single element).
- for values in read_spin_data(file_data=[line],
spin_id_col=spin_id_col, mol_name_col=mol_name_col, res_num_col=res_num_col,
res_name_col=res_name_col, spin_num_col=spin_num_col,
spin_name_col=spin_name_col, data_col=data_col[i], sep=sep, spin_id=spin_id):
+ for values in read_spin_data(file_data=[line],
spin_id_col=spin_id_col, mol_name_col=mol_name_col, res_num_col=res_num_col,
res_name_col=res_name_col, spin_num_col=spin_num_col,
spin_name_col=spin_name_col, data_col=data_col[i], sep=sep, spin_id=spin_id,
raise_flag=False):
+ # The data flag.
+ data_flag = True
+
# Check the values.
if len(values) != 6 and data_present:
raise RelaxError("The molecule name, residue number and
name, spin number and name, and value columns could not be found in the data
%s." % repr(values))
@@ -133,7 +137,8 @@
mol_name, res_num, res_name, spin_num, spin_name = values
# Add the assignment to the peak list object.
- peak_list.add(mol_names=[mol_name, mol_name], res_nums=[res_num,
res_num], res_names=[res_name, res_name], spin_nums=[spin_num, spin_num],
spin_names=[spin_name, spin_name], intensity=intensity)
+ if data_flag:
+ peak_list.add(mol_names=[mol_name, mol_name], res_nums=[res_num,
res_num], res_names=[res_name, res_name], spin_nums=[spin_num, spin_num],
spin_names=[spin_name, spin_name], intensity=intensity)
def read_peak_list(file=None, dir=None, int_col=None, spin_id_col=None,
mol_name_col=None, res_num_col=None, res_name_col=None, spin_num_col=None,
spin_name_col=None, sep=None, spin_id=None):
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